---
title: "Busara Dashboard"
author: "Rémi Thériault"
output:
flexdashboard::flex_dashboard:
orientation: columns
vertical_layout: fill
social: menu
source_code: embed
# theme: lumen
storyboard: false
params:
API_TOKEN_PUBMED: API_TOKEN_PUBMED
---
```{r setup, include=FALSE}
library(flexdashboard)
query_pubmed <- TRUE
```
```{r packages}
# Load packages
library(extrafont)
library(easyPubMed)
library(dplyr)
library(purrr)
library(stringr)
library(stringi)
library(DT)
library(fuzzyjoin)
library(countrycode)
library(Ecfun)
library(tidyr)
library(waffle)
library(plotly)
library(ggplot2)
library(ggflags)
library(knitr)
library(lubridate)
library(xts)
library(tibble)
library(dygraphs)
library(rempsyc)
library(RColorBrewer)
```
```{r API_TOKEN_PUBMED, eval=query_pubmed}
# API_TOKEN_PUBMED <- keyring::key_get("pubmed", "rempsyc")
# API_TOKEN_PUBMED <- Sys.getenv("API_TOKEN_PUBMED")
API_TOKEN_PUBMED <- params$API_TOKEN_PUBMED
if (API_TOKEN_PUBMED == "") stop("API_TOKEN_PUBMED is an empty string. Terminating workflow.")
if (nchar(API_TOKEN_PUBMED) != 36) stop("API_TOKEN_PUBMED is not 36 characters-long. Terminating workflow.")
```
```{r batch_pubmed_download, results='hide', eval=query_pubmed}
# Download data
d.fls <- batch_pubmed_download(
pubmed_query_string = paste(
"Developmental Psychology [Journal]",
"OR Journal of Personality and Social Psychology [Journal]",
"OR Journal of Abnormal Psychology [Journal]",
"OR Journal of Family Psychology [Journal]",
"OR Health Psychology [Journal]",
"OR Journal of Educational Psychology [Journal]",
"AND ('2021/01/01'[Date - Publication] : '3000/12/31'[Date - Publication])"
),
dest_file_prefix = "data/easyPubMed_data_",
api_key = API_TOKEN_PUBMED,
batch_size = 5000)
```
```{r all_articles_to_df, eval=query_pubmed}
# Convert XLM data to a data frame of first authors
# articles.df <- table_articles_byAuth(d.fls, included_authors = "first")
all_articles_to_df <- function(d.fls){
y <- lapply(seq_along(d.fls), function(x) {
list.articles <- articles_to_list(d.fls[x])
list.articles.df <- lapply(list.articles, article_to_df)
articles.df <- do.call(rbind, list.articles.df)
})
do.call(rbind, y)
}
articles.df <- all_articles_to_df(d.fls)
articles.df <- articles.df %>%
filter(!duplicated(pmid))
```
```{r address_split, message=FALSE, warning=FALSE, eval=query_pubmed}
# Split address in university and department
addr.split <- str_split(articles.df$address, ",")
split_address <- function(addr.split, string) {
ind1 <- map(addr.split, ~which(grepl(string, .x)))
ind1 <- imap(addr.split, \(x, idx) pluck(ind1[[idx]])[1])
ind1 <- imap(addr.split, \(x, idx) pluck(x, ind1[[idx]]))
ind1 <- trimws(as.character(ind1))
ind1 <- replace(ind1, ind1 == "NULL", NA)
}
string.dep <- "Department|Faculty|Center|School|Unit|Institute|Centre|Division|Unidad"
dep <- split_address(addr.split, string.dep)
string.uni <- "University"
uni <- split_address(addr.split, string.uni)
string.uni2 <- "University|College|School|Institute|Center|Centre|CEMIC, CONICET|CNRS|INSEAD"
uni2 <- split_address(addr.split, string.uni2)
uni3 <- ifelse(!is.na(uni), uni, uni2)
articles.df <- articles.df %>%
mutate(department = dep,
university = uni3)
articles.df <- articles.df %>%
select(journal, year, university, department, address, lastname, firstname,
month, day, jabbrv, title, doi, pmid, abstract)
```
```{r correct_universities, eval=query_pubmed}
# Correct a few university names manually
articles.df <- articles.df %>%
mutate(university = case_when(
university == "Stony Brook University" ~ "University of Colorado at Colorado Springs",
university == "Technion-Israel Institute of Technology" ~ "Technion - Israel Institute of Technology",
university == "University of Montreal" ~ "Université de Montréal",
university == "Philipps-University of Marburg" ~ "Phillips-Universität Marburg",
university == "University of Wisconsin-Madison" ~ "University of Wisconsin - Madison",
TRUE ~ university
))
```
```{r countries_data, eval=query_pubmed}
# Download university + country data
countries <- read.csv(
"https://raw.githubusercontent.com/endSly/world-universities-csv/master/world-universities.csv",
header = FALSE)
names(countries) <- c("country_code", "university", "website")
countries <- countries[1:2]
# Correct/add a few university countries manually
countries <- countries %>%
mutate(
country_code = replace(country_code,
university == "University of the Netherlands Antilles, Curacao", "CW"),
country_code = replace(country_code,
university == "University of Sint Eustatius School of Medicine", "SX"),
country_code = replace(country_code,
university == "St.James's School of Medicine, Bonaire" |
university == "American University of the Caribbean, Sint Maarten" |
university == "International University School of Medicine (IUSOM)", "BQ")) %>%
add_row(country_code = "US", university = "University of Colorado") %>%
add_row(country_code = "US", university = "Stony Brook University") %>%
add_row(country_code = "GB", university = "York St John University") %>%
add_row(country_code = "DE", university = "Max Planck Institute for Human Development") %>%
add_row(country_code = "AR", university = "CEMIC, CONICET") %>%
add_row(country_code = "VN", university = "SWPS University of Social Sciences and Humanities") %>%
add_row(country_code = "SG", university = "Yale-NUS College") %>%
add_row(country_code = "US", university = "Rutgers Business School-Newark and New Brunswick") %>%
add_row(country_code = "BR", university = "Institute D'Or for Research and Teaching") %>%
add_row(country_code = "GB", university = "Moray House School of Education and Sport") %>%
add_row(country_code = "AU", university = "Institute for Positive Psychology and Education") %>%
add_row(country_code = "FR", university = "CNRS") %>%
add_row(country_code = "US", university = "Columbia Business School") %>%
add_row(country_code = "US", university = "Office of Population Research") %>%
add_row(country_code = "US", university = "School of Family Life") %>%
add_row(country_code = "CH", university = "Jacobs Center for Productive Youth Development") %>%
add_row(country_code = "KR", university = "SKK Graduate School of Business") %>%
add_row(country_code = "SG", university = "Lee Kong Chian School of Business") %>%
add_row(country_code = "US", university = "Tepper School of Business") %>%
add_row(country_code = "US", university = "Stephen M. Ross School of Business") %>%
add_row(country_code = "US", university = "Fuqua School of Business") %>%
add_row(country_code = "US", university = "Jones Graduate School of Business") %>%
add_row(country_code = "US", university = "Questrom School of Business") %>%
add_row(country_code = "US", university = "Booth School of Business") %>%
add_row(country_code = "FR", university = "INSEAD") %>%
add_row(country_code = "BE", university = "University of Liege") %>%
add_row(country_code = "KR", university = "Sungkyunkwan University") %>%
add_row(country_code = "DE", university = "University of Tubingen") %>%
add_row(country_code = "AU", university = "Melbourne School of Psychological Sciences") %>%
add_row(country_code = "AT", university = "University of Vienna") %>%
add_row(country_code = "NL", university = "Vrije Universiteit Amsterdam") %>%
add_row(country_code = "CA", university = "Montreal Behavioural Medicine Centre (MBMC)") %>%
add_row(country_code = "GB", university = "Manchester Centre for Health Psychology") %>%
add_row(country_code = "US", university = "Annenberg School for Communication and Journalism") %>%
add_row(country_code = "US", university =
"National Center for Posttraumatic Stress Disorder at VA Boston Healthcare System") %>%
add_row(country_code = "US", university = "Cincinnati Children's Hospital Medical Center") %>%
add_row(country_code = "US", university = "University of Wisconsin")
# Custom function for two-sided vlookup
partial_vlookup <- function(pattern, lookup_vector) {
out <- map_chr(pattern, \(x) {
out <- grep(x, lookup_vector, value = TRUE, fixed = TRUE)[1]
if (is.na(out)) {
out <- rgrep(lookup_vector, x, value = TRUE, fixed = TRUE)[1]
}
out
})
out
}
```
```{r partial_vlookup, eval=query_pubmed}
# Match universities and countries
articles.df2 <- articles.df %>%
mutate(
university_old = university,
university = partial_vlookup(university, countries$university),
university = ifelse(is.na(university), partial_vlookup(address, countries$university), university),
.after = university)
articles.df3 <- articles.df2 %>%
left_join(countries, by = "university", multiple = "first") %>%
relocate(country_code, .after = year)
```
```{r country_code_conversion, eval=query_pubmed}
# Get full name country, continent, and region
articles.df4 <- articles.df3 %>%
mutate(doi = paste0("https://doi.org/", doi),
country = countrycode(country_code, "genc2c", "country.name"),
region = countrycode(country_code, "genc2c", "un.regionsub.name"),
continent = countrycode(country_code, "genc2c", "continent"),
continent = case_when(continent == "Americas" ~ region,
TRUE ~ continent),
.after = country_code) %>%
mutate(date = paste(year, month, day, sep = "-"),
date = as_date(date)) %>%
ungroup() %>%
mutate()
```
# Continent
## Column 1 {data-width=2150}
### Waffle plot of journal paper percentages, by continent (each square = 1% of data) {data-height=600}
```{r continent_waffle_overall}
articles.df4 <- readRDS("articles.df4.rds")
continent.order <- c("Northern America", "Europe", "Asia", "Oceania", "Latin America and the Caribbean", "Africa")
continent.order.short <- c("North America", "Europe", "Asia", "Oceania", "Latin America", "Africa")
articles.df4 <- articles.df4 %>%
mutate(continent = factor(continent, levels = continent.order),
journal = gsub(":.*", "", journal))
df.continent <- articles.df4 %>%
mutate(missing = sum(is.na(continent))/n()) %>%
filter(!is.na(continent)) %>%
summarize(Papers = n(),
`North America` = sum(continent == "Northern America")/n(),
Europe = sum(continent == "Europe")/n(),
Asia = sum(continent == "Asia")/n(),
Oceania = sum(continent == "Oceania")/n(),
`Latin America` = sum(continent == "Latin America and the Caribbean")/n(),
Africa = sum(continent == "Africa")/n(),
Missing = first(missing),
) %>%
mutate(across(`North America`:Missing, ~ .x * 100)) # %>%
# mutate(across(`North America`:Missing, ~ round(.x, 2))) %>%
# rename_with(str_to_title) %>%
# rename(`Missing*` = Missing) %>%
# datatable(#extensions = 'Responsive',
# options = list(searching = FALSE, paging = FALSE),
# caption = "Journal paper percentages, by continent")
# data.waffle <- set_names(as.numeric(t(df.continent[2:7])), names(df.continent[2:7]))
data.waffle <- articles.df4 %>%
mutate(missing = sum(is.na(continent))/n()) %>%
filter(!is.na(continent)) %>%
group_by(continent) %>%
add_count(name = "Papers") %>%
ungroup() %>%
mutate(nrow = n()) %>%
count(continent, nrow, sort = TRUE, name = "Papers") %>%
mutate(continent = case_match(
continent,
continent.order[1] ~ continent.order.short[1],
continent.order[5] ~ continent.order.short[5],
continent ~ continent),
Percentage = Papers / nrow * 100) %>%
select(-c(nrow, Papers)) %>%
rename_with(str_to_title, .cols = 1)
waffle(data.waffle, legend_pos = "right") +
theme(legend.text = element_text(size = 15)) #+ # rows = 5,
#coord_cartesian(ylim=c(0,2))#%>%
#ggplotly()
```
### Table of journal paper percentages, by continent {data-height=200}
```{r, continent_table}
df.continent %>%
mutate(across(`North America`:Missing, ~ round(.x, 2))) %>%
rename_with(str_to_title) %>%
rename(`Missing*` = Missing) %>%
datatable(#extensions = 'Responsive',
options = list(searching = FALSE, paging = FALSE),
caption = "Journal paper percentages, by continent")
```
## Column 2 {.tabset .tabset-fade}
### Context
**Representativity of First Authors in Psychology**
A large proportion of first authors in psychology are located in North America or Europe, mostly in the US (Thalmayer et al., 2021, Arnett, 2008). In this dashboard, I present some aggregated data by continent, country, year, and journal (for first authors only).
> \* Percentages are calculated after excluding missing values. The *Missing* column shows the real percentage of missing values.
### Method & Data
The data from this report include information about publications from one of six psychology journals (*Developmental Psychology*, *Journal of Personality and Social Psychology*, *Journal of Abnormal Psychology*, *Journal of Family Psychology*, *Health Psychology*, and *Journal of Educational Psychology*) for years 2015 to 2023. They include information about the articles (e.g., title, abstract) as well as on the authors, such as university of affiliation. I have obtained these data from PubMed using the PubMed API through the `easyPubMed` package. I have determined the country of the first author of each paper based on the affiliation address by matching the university name with a world university names database obtained from GitHub.
> \* Percentages are calculated after excluding missing values. The *Missing* column shows the real percentage of missing values.
### Missing data
Some of the papers were missing address information; in many cases, the PubMed API provided only the department and no university. It was not possible to identify the country in these cases (one would need to look at the actual papers one by one to make manual corrections). Furthermore, some university names from the data did not match the university name database obtained from GitHub. In some cases, I have brought manual corrections to university names in an attempt to reduce the number of missing values.
> \* Percentages are calculated after excluding missing values. The *Missing* column shows the real percentage of missing values.
### Next Steps
Possible future steps include: (a) obtaining a better, more current university name database (that includes country of university), (b) making manual corrections for other research institutes not included in the university database, and (c) automatically updating the data every week or so.
(PubMed API Key character length = `r nchar(API_TOKEN_PUBMED)`)
> \* Percentages are calculated after excluding missing values. The *Missing* column shows the real percentage of missing values.
# Continent, by Year
## Column 1 {data-width=800}
### Scatter plot of journal paper percentages, by continent and year {data-height=600}
```{r, continent_scatter_overall}
df.continent2 <- articles.df4 %>%
mutate(missing = sum(is.na(continent))/n()) %>%
filter(!is.na(continent)) %>%
group_by(year) %>%
summarize(`North America` = sum(continent == "Northern America")/n(),
Europe = sum(continent == "Europe")/n(),
Asia = sum(continent == "Asia")/n(),
Oceania = sum(continent == "Oceania")/n(),
`Latin America` = sum(continent == "Latin America and the Caribbean")/n(),
Africa = sum(continent == "Africa")/n(),
) %>%
mutate(across(2:6, ~ .x * 100)) %>%
arrange(year)
df.continent3 <- df.continent2 %>%
pivot_longer(-year, names_to = "continent", values_to = "papers_percentage") %>%
mutate(year = as.numeric(year), continent = factor(continent, levels = continent.order.short),
papers_percentage = round(papers_percentage))
colors <- suppressWarnings(RColorBrewer::brewer.pal(length(unique(df.continent3$continent)), "Set2"))
nice_scatter(df.continent3,
predictor = "year",
response = "papers_percentage",
group = "continent",
colours = colors,
method = "loess",
groups.order = "decreasing",
ytitle = "% of All Papers") %>%
ggplotly(tooltip = c("x", "y"))
```
## Column 2
### Table of journal paper percentages, by continent {data-height=200}
```{r, continent_table_journal_year}
continent.paper.missing <- articles.df4 %>%
group_by(year) %>%
summarize(Missing = sum(is.na(continent))/n()) %>%
pull(Missing)
articles.df4 %>%
mutate(missing = sum(is.na(continent))/n()) %>%
filter(!is.na(continent)) %>%
group_by(year) %>%
summarize(Papers = n(),
`North America` = sum(continent == "Northern America")/n(),
Europe = sum(continent == "Europe")/n(),
Asia = sum(continent == "Asia")/n(),
Oceania = sum(continent == "Oceania")/n(),
`Latin America` = sum(continent == "Latin America and the Caribbean")/n(),
Africa = sum(continent == "Africa")/n(),
`Missing*` = first(missing),
) %>%
mutate(`Missing*` = continent.paper.missing[-1],
across(`North America`:`Missing*`, ~ round(.x * 100, 2))) %>%
arrange(desc(year)) %>%
rename_with(str_to_title) %>%
datatable(caption = "Journal paper percentages, by continent and year")
```
> \* Percentages are calculated after excluding missing values. The *Missing* column shows the real percentage of missing values.
# Continent, by Journal
## Column 1 {data-width=700}
### Waffle plot of journal paper percentages, by continent and journal (each square = 1% of data) {data-height=600}
```{r continent_table_journal_figure}
df.continent5 <- articles.df4 %>%
mutate(missing = sum(is.na(continent))/n()) %>%
filter(!is.na(continent)) %>%
group_by(journal) %>%
summarize(`North America` = sum(continent == "Northern America")/n(),
Europe = sum(continent == "Europe")/n(),
Asia = sum(continent == "Asia")/n(),
Oceania = sum(continent == "Oceania")/n(),
`Latin America` = sum(continent == "Latin America and the Caribbean")/n(),
Africa = sum(continent == "Africa")/n(),
) %>%
mutate(across(2:6, ~ .x * 100)) %>%
arrange(journal)
df.continent6 <- df.continent5 %>%
pivot_longer(-journal, names_to = "continent", values_to = "number") %>%
mutate(continent = factor(continent, levels = continent.order.short))
df.continent6 %>%
ggplot(aes(fill = continent, values = number)) +
geom_waffle(color = "white", size = 0.8, na.rm = TRUE) +
facet_wrap(~journal) +
scale_y_continuous(expand=c(0,0)) +
coord_equal() +
theme_minimal(base_size=6) +
theme(panel.grid = element_blank(),
axis.text = element_blank(),
plot.title=element_text(hjust=0.5),
legend.title = element_blank(),
legend.text = element_text(size = 5)) +
ggplot2::scale_fill_manual(values = colors)
```
## Column 2
### Table of journal paper percentages, by continent and journal {data-height=200}
```{r continent_table_journal}
journal.paper.missing <- articles.df4 %>%
group_by(journal) %>%
summarize(Missing = sum(is.na(continent))/n()) %>%
pull(Missing)
articles.df4 %>%
mutate(missing = sum(is.na(continent))/n()) %>%
filter(!is.na(continent)) %>%
group_by(journal) %>%
summarize(Papers = n(),
`North America` = sum(continent == "Northern America")/n(),
Europe = sum(continent == "Europe")/n(),
Asia = sum(continent == "Asia")/n(),
Oceania = sum(continent == "Oceania")/n(),
`Latin America` = sum(continent == "Latin America and the Caribbean")/n(),
Africa = sum(continent == "Africa")/n(),
`Missing*` = first(missing),
) %>%
mutate(`Missing*` = journal.paper.missing,
across(`North America`:`Missing*`, ~ round(.x * 100, 2))) %>%
rename_with(str_to_title) %>%
datatable(caption = "Journal paper percentages, by continent and journal")
```
> \* Percentages are calculated after excluding missing values. The *Missing* column shows the real percentage of missing values.
# Country
## Column 1 {data-width=800}
### Waffle plot of journal paper percentages, by country (each flag = 1% of data)
```{r country_table_overall, fig.width=4.5, fig.height=4.5}
df.country <- articles.df4 %>%
mutate(missing = sum(is.na(country_code))/n()) %>%
filter(!is.na(country_code)) %>%
mutate(nrow = n()) %>%
count(country, country_code, nrow, sort = TRUE, name = "Papers") %>%
mutate(Percentage = Papers / nrow) %>%
select(-nrow) %>%
add_row(country = "Missing*",
Papers = sum(is.na(articles.df4$country)),
Percentage = sum(is.na(articles.df4$country)) / nrow(articles.df4),
.before = 1) %>%
rename_with(str_to_title)
df.country3 <- articles.df4 %>%
mutate(missing = sum(is.na(country))/n()) %>%
filter(!is.na(country)) %>%
group_by(country) %>%
add_count(name = "Papers") %>%
mutate(Percentage = Papers / nrow(.),
country = case_when(
Percentage < 0.02 ~ "Other",
TRUE ~ country)
) %>%
ungroup() %>%
mutate(nrow = n()) %>%
count(country, nrow, sort = TRUE, name = "Papers") %>%
mutate(Percentage = Papers / nrow * 100) %>%
select(-c(nrow, Papers)) %>%
rename_with(str_to_title, .cols = 1)
colours.country <- colorRampPalette(colors)(length(df.country3$Country))
# waffle(df.country3, legend_pos = "right", colors = colours.country) +
# theme(legend.text = element_text(size = 15))
waffle_flags <- function(in_map_var, len_x = NA, na_flag = "ac"){
in_map_var <- data.frame(country = in_map_var)
my_prop <- in_map_var %>%
count(country, sort = TRUE) %>%
mutate(n2 = round(n / nrow(in_map_var) * 100))
in_map_var <- lapply(seq_len(nrow(my_prop)), \(x) {
rep(my_prop$country[x], my_prop$n2[x])}) %>%
unlist
# work out grid dimensions
var_count <- length(in_map_var)
if(is.na(len_x)){
x_count <- ceiling(sqrt(var_count))
} else {
x_count <- len_x
}
y_count <- ceiling(var_count / x_count)
grid_count <- x_count * y_count
df <-
data.frame(x = rep(1:y_count, each = x_count),
y = rep(1:x_count, y_count),
country = c(in_map_var, rep(na_flag, grid_count - var_count))
)
country_4legend <- unique(df$country)[unique(df$country) != na_flag]
p <-
ggplot(df, aes(x, y, country = country)) +
geom_flag(size = 8.5) +
scale_country(breaks = country_4legend) +
theme_void() +
theme(legend.position = "right")
if(grid_count > var_count){
p <-
p +
geom_point(data = df[var_count:grid_count, ], aes(x, y), colour = "white", size = 10)
}
return(p)
}
my_prop <- df.country3 %>%
mutate(Country = countrycode(Country, "country.name", "genc2c"),
Country = tolower(Country)) %>%
filter(!is.na(Country))
in_map_var <- lapply(seq_len(nrow(my_prop)), \(x) {
rep(my_prop$Country[x], my_prop$Percentage[x])}) %>%
unlist
waffle_flags(in_map_var)
```
## Column 2
### Table of journal paper percentages, by country {data-height=200}
```{r country_table_journal}
df.country %>%
mutate(Percentage = round(Percentage * 100, 2)) %>%
rename(`Country Code` = Country_code) %>%
datatable(caption = "Journal paper percentages, by country")
```
> \* Percentages are calculated after excluding missing values. The *Missing* row shows the real percentage of missing values.
# Country, by Year
## Column 1 {data-width=1000}
### Time series plot of journal paper percentages, by country and year
```{r, country_series_year}
df.country.year.papers <- articles.df4 %>%
filter(!is.na(country)) %>%
count(year, name = "Papers") %>%
arrange(desc(year), desc(Papers))
get_year_papers <- function(year) {
df.country.year.papers[which(
df.country.year.papers$year == year), "Papers"]
}
df.country.year.missing <- articles.df4 %>%
filter(is.na(country)) %>%
group_by(year) %>%
count(year, name = "Papers") %>%
arrange(desc(year), desc(Papers)) %>%
left_join(by = "year", articles.df4 %>%
group_by(year) %>%
count(year, name = "all_papers") %>%
arrange(desc(year))) %>%
mutate(percentage = round(Papers / all_papers * 100, 2),
country = "Missing*") %>%
select(-all_papers)
df.country.year <- articles.df4 %>%
group_by(year, country) %>%
filter(!is.na(continent)) %>%
count(name = "Papers") %>%
mutate(percentage = round(Papers / get_year_papers(year) * 100, 2))
df.country.year2 <- df.country.year %>%
ungroup() %>%
add_row(df.country.year.missing) %>%
arrange(desc(year), desc(Papers))
# getPalette = colorRampPalette(brewer.pal(8, "Set2"))
# colors <- getPalette(length(unique(df.country.year$country)))
# df.country.year %>%
# mutate(year = as.numeric(year),
# country = as.factor(country)) %>%
# nice_scatter(
# predictor = "year",
# response = "percentage",
# group = "country",
# colours = colors,
# method = "lm",
# groups.order = "decreasing",
# ytitle = "% of All Papers") %>%
# ggplotly(tooltip = c("x", "y"))
# Include flags on scatter plot
# Note: doesn't work with ggplotly it seems
# library(ggflags)
# df.country.year %>%
# mutate(year = as.numeric(year),
# country = countrycode(country, "country.name", "genc2c"),
# country = tolower(country),
# country = as.factor(country)) %>%
# nice_scatter(
# predictor = "year",
# response = "percentage",
# group = "country",
# colours = colors,
# method = "lm",
# groups.order = "decreasing",
# ytitle = "% of All Papers") +
# geom_flag(aes(country = country)) +#%>%
# scale_country(aes(country = country)) #%>%
#ggplotly(tooltip = c("x", "y"))
q <- df.country.year %>%
ungroup() %>%
select(year, country, percentage) %>%
mutate(year = as.Date(year, "%Y")) %>%
pivot_wider(names_from = country, values_from = percentage) %>%
as.xts
dygraph(q) %>%
dyRangeSelector() %>%
dyUnzoom() %>%
dyCrosshair(direction = "vertical") %>%
dyOptions(strokeWidth = 3)
```
## Column 2
### Table of journal paper percentages, by country and year {data-height=200}
```{r, country_table_year}
df.country.year2 %>%
rename_with(str_to_title) %>%
datatable(caption = "Journal paper percentages, by country and year")
```
> \* Percentages are calculated after excluding missing values. The *Missing* column shows the real percentage of missing values.
# Country, by Journal
## Column 1 {data-width=800}
### Waffle plot of journal paper percentages, by continent and journal (each square = 1% of data) {data-height=600}
```{r country_table_journal_figure}
# df.country.journal.missing <- articles.df4 %>%
# filter(!is.na(country)) %>%
# count(journal, country, name = "Papers") %>%
# arrange(desc(journal), desc(Papers))
#
# get_journal_papers <- function(journal, country) {
# df.country.journal.missing[which(
# df.country.journal.missing$journal == journal &
# df.country.journal.missing$country == country), "Papers"]
# }
df.country.journal.missing2 <- articles.df4 %>%
filter(!is.na(country)) %>%
count(journal, name = "Papers") %>%
arrange(desc(journal), desc(Papers))
get_journal_papers2 <- function(journal) {
df.country.journal.missing2[which(
df.country.journal.missing2$journal == journal), "Papers"]
}
df.country.journal <- articles.df4 %>%
filter(!is.na(country)) %>%
group_by(journal, country) %>%
add_count(name = "Papers") %>%
mutate(percentage = Papers / nrow(.),
country = case_when(
percentage < 0.01 ~ "Other",
TRUE ~ country)
) %>%
ungroup() %>%
count(journal, country, sort = TRUE, name = "Papers") %>%
rowwise %>%
mutate(percentage = round(Papers / get_journal_papers2(journal) * 100, 2),
country = as.factor(country)) %>%
arrange(desc(journal), desc(Papers))
# colours.country2 <- colorRampPalette(colors)(unique(df.country.journal$country))
df.country.journal %>%
ggplot(aes(fill = country, values = percentage)) +
geom_waffle(color = "white", size = 0.8, na.rm = TRUE) +
facet_wrap(~journal) +
scale_y_continuous(expand=c(0,0)) +
coord_equal() +
theme_minimal(base_size=6) +
theme(panel.grid = element_blank(),
axis.text = element_blank(),
plot.title=element_text(hjust=0.5),
legend.title = element_blank(),
legend.text = element_text(size = 5)) +
ggplot2::scale_fill_manual(values = colours.country)
```
## Column 2
### Table of journal paper percentages, by country and journal {data-height=200}
```{r country_table_journal2}
df.country.journal2 <- articles.df4 %>%
group_by(journal, country) %>%
filter(!is.na(country)) %>%
count(name = "Papers") %>%
mutate(percentage = round(Papers / get_journal_papers2(journal) * 100, 2)) %>%
arrange(desc(journal), desc(Papers))
df.country.journal2 %>%
rename_with(str_to_title) %>%
datatable(caption = "Journal paper percentages, by country and year")
```
> \* Percentages are calculated after excluding missing values. The *Missing* column shows the real percentage of missing values.
